id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2998 Clipper symmetry: self.structure is None chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.91 (2019-08-27) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-08-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b4.dev0-cp37-cp37m-win_amd64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\arhue\appdata\local\ucsf\chimerax\cache\0.91\installers\chimerax_isolde-1.0b4.dev0-cp37-cp37m-win_amd64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- ISOLDE==1.0b4.dev0) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX- ISOLDE==1.0b4.dev0) (0.91) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.10.* in c:\users\arhue\appdata\local\ucsf\chimerax\0.91\site-packages (from ChimeraX- ISOLDE==1.0b4.dev0) (0.10.0) Installing collected packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b4.dev0 Uninstalling ChimeraX-ISOLDE-1.0b4.dev0: Successfully uninstalled ChimeraX-ISOLDE-1.0b4.dev0 Successfully installed ChimeraX-ISOLDE-1.0b4.dev0 Lock 2321031843208 acquired on C:\Users\arhue\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock Lock 2321031843208 released on C:\Users\arhue\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock WARNING: You are using pip version 19.2.1, however version 20.0.2 is available. You should consider upgrading via the 'python -m pip install --upgrade pip' command. > toolshed show ISOLDE > set selectionWidth 4 Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield > open 6out Summary of feedback from opening 6out fetched from pdb --- note | Fetching compressed mmCIF 6out from http://files.rcsb.org/download/6out.cif 6out title: Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP asymmetric unit in T=3 symmetry [more info...] Chain information for 6out #1 --- Chain | Description A B C | Capsid protein VP1 6out title: Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP asymmetric unit in T=3 symmetry [more info...] Chain information for 6out --- Chain | Description 1.1/A 1.1/B 1.1/C | Capsid protein VP1 Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time > close #1.1 > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #2 --- Chain | Description A B C | capsid protein VP1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 2.1/A 2.1/B 2.1/C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Summary of feedback from opening 20205 fetched from emdb --- note | Fetching compressed map 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 Invalid ""toModel"" argument: Must specify 1 structure, got 0 for ""#1"" Invalid ""toModel"" argument: Must specify 1 structure, got 0 for ""#1"" > clipper associate #2 toModel #2.1 > clipper associate #3 toModel #2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1382, in _box_moved_cb self._update_box() File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1382, in _box_moved_cb self._update_box() File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1382, in _box_moved_cb self._update_box() File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1382, in _box_moved_cb self._update_box() File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1382, in _box_moved_cb self._update_box() File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1382, in _box_moved_cb self._update_box() File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms AttributeError: 'NoneType' object has no attribute 'atoms' Error processing trigger ""spotlight moved"": AttributeError: 'NoneType' object has no attribute 'atoms' File ""C:\Users\arhue\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\clipper\symmetry.py"", line 1395, in _update_box atoms = self.structure.atoms See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 419.72 OpenGL renderer: GeForce GTX 1060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party 0.91 fixed all ChimeraX